Article ID: 1652 - Last Modified: February 9, 2012

When state penalties are being applied, why isn’t the “docking score” always the sum of the Epik “State penalty” and the GlideScore (“glide gscore”)?

In general the “docking score” is almost always the sum of the GlideScore (“glide gscore”) and the Epik “State Penalty”. However, there are cases when this will not be true. If Epik has generated a metal-binding ligand variant, one or more atom-level “Metal State Penalty” properties will be stored, in addition to the regular structure-level Epik “State Penalty”, which includes the smallest structure-level “Metal State Penalty.”

If a ligand pose binds to a metal during Glide docking, the “Metal State Penalty” value for the ligand interaction is applied directly to the “docking score” instead of the normal Epik “State Penalty”. If during docking the ligand has multiple metal-binding atoms, the effective state penalty applied by Glide can be different from either the structure-level “State Penalty” or the “Metal State Penalty”. Please note, that since the actual penalty applied depends on the specific interactions between the ligand and the receptor, penalties applied to a specific ligand will vary across different poses.

Related Articles:

#27: What is the DockingScore and how do I use it?#723: How well does Glide deal with binding sites containing metal ions for docking?#1487: What are the "metal-binding states" produced by Epik, and how are they used?